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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Multiple signal classification as a blind reconstruction approach for three-dimensional structured illumination microscopy |
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Identification Number: |
doi:10.18710/3POVDT |
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Distributor: |
DataverseNO |
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Date of Distribution: |
2023-05-31 |
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Version: |
1 |
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Bibliographic Citation: |
Opstad, Ida, 2023, "Replication Data for: Multiple signal classification as a blind reconstruction approach for three-dimensional structured illumination microscopy", https://doi.org/10.18710/3POVDT, DataverseNO, V1 |
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Citation |
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Title: |
Replication Data for: Multiple signal classification as a blind reconstruction approach for three-dimensional structured illumination microscopy |
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Identification Number: |
doi:10.18710/3POVDT |
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Authoring Entity: |
Opstad, Ida (UiT The Arctic University of Norway) |
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Other identifications and acknowledgements: |
Acuña, Sebastian |
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Other identifications and acknowledgements: |
Agarwal, Krishna |
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Other identifications and acknowledgements: |
Birgisdottir, Åsa B. |
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Other identifications and acknowledgements: |
Ahluwalia, Balpreet S. |
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Other identifications and acknowledgements: |
Smart, Katie |
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Producer: |
UiT The Arctic University of Norway |
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Software used in Production: |
SoftWoRx |
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Software used in Production: |
Python |
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Software used in Production: |
ImageJ/Fiji |
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Grant Number: |
Tematiske satsinger (VirtualStain; project number 2061348 |
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Distributor: |
DataverseNO |
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Distributor: |
UiT The Arctic University of Norway |
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Access Authority: |
Opstad, Ida |
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Access Authority: |
Agarwal, Krishna |
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Depositor: |
Opstad, Ida Sundvor |
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Date of Deposit: |
2023-05-16 |
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Holdings Information: |
https://doi.org/10.18710/3POVDT |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, super-resolution, 3DSIM, structured illumination microscopy, MUSICAL, multiple signal classification algorithm, mitochondria, kidney, computational nanoscopy |
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Abstract: |
The dataset contains replication data for the research paper "Multiple signal classification as a blind reconstruction approach for three-dimensional structured illumination microscopy" (3DSIM). The paper compares image reconstructions using conventional 3DSIM and two variants of "Multiple signal classification algorithm" (MUSICAL), MUS-S and MUS-CE. <p> This dataset provides 1 image generated of mitochondria in living cells, 1 image of mitochondria in fixed cells, 1 image of nephrin in fixed murine kidney tissue using 3DSIM, MUS-S and MUS-CE. The 3DSIM raw data and reconstructions for H9c2 cells are available from https://doi.org/10.18710/PDCLAS. <p> Four different types of image data are included: -Raw structured illumination kidney data used for all super-resolution image reconstructions (i.e., MUS-S, MUS-CE and 3DSIM) -3DSIM images of a kidney section. -MUS-S for kidney, fixed and live H9c2 cardiomyoblasts -MUS-CE for kidney, fixed and live H9c2 cardiomyoblasts <p> The data is organized in different folders according to sample type (FixedCell/LiveCell H9c2, KidneyTissue), and reconstruction method (MUS-CE, MUS-S, 3DSIM). The image files are TIFF images. <p> Abbreviations:<p> 3DSIM - three-dimensional structured illumination microscopy<p> MUSICAL - Multiple signal classification algorithm<p> MUS-S - soft thresholding variant of MUSICAL<p> MUS-CE - contrast enhancement, a low-resolution variant of MUSICAL<p> LTDR - LysoTracker Deep Red<p> MAX - maximum intensity z-projected three-dimensional images<p> c or ch - channel<p> |
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Time Period: |
2018-06-06-2023-05-05 |
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Date of Collection: |
2018-12-12-2020-05-11 |
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Country: |
Norway |
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Geographic Coverage: |
Troms, Tromsø |
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Kind of Data: |
super-resolution fluorescence microscopy |
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Kind of Data: |
experimental |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Notes: |
<a href="http://creativecommons.org/publicdomain/zero/1.0">CC0 1.0</a> |
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Other Study Description Materials |
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Related Studies |
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Opstad, Ida S., 2021, "3DSIM data of mitochondria in the cardiomyoblast cell-line H9c2 adapted to either glucose or galactose", https://doi.org/10.18710/PDCLAS, DataverseNO |
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Related Publications |
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Citation |
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Title: |
Submitted for review |
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Bibliographic Citation: |
Submitted for review |
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Label: |
00_ReadMe.txt |
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Notes: |
text/plain |
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Label: |
0_file_organization_fixed-cells-H9c2.png |
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Notes: |
image/png |
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Label: |
0_file_organization_kidney-tissue.png |
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Notes: |
image/png |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch1_CE-stack-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch1_CE-stack.tif |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch1_CE-stack-downscaled.tif |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch1_CE-stack.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch2_CE-stack-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch2_CE-stack.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch2_CE-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch2_CE.tif |
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image/tiff |
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20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch3_CE-stack-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch3_CE-stack.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch3_CE-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch3_CE1s.tif |
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image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch1_MUSS-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch1_MUSS.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch1_MUSS-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch1_MUSS.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch2_MUSS-stack-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch2_MUSS-stack.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch2_MUSS-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch2_MUSS.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch3_MUSS-stack-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch3_MUSS-stack.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch3_MUSS-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_PFA4-GA02_LTDR100nm-40m_1520_sim512_003_ch3_MUSS.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20181212_KideneySections_AF488_1512_sim1024_029.log |
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Notes: |
text/plain |
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20181212_KideneySections_AF488_1512_sim1024_029.tif |
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image/tiff |
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20181212_KideneySections_AF488_1512_sim1024_029_SIR.tif |
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Notes: |
image/tiff |
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20181212_KideneySections_AF488_1512_sim1024_029_SIR_log.txt |
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Notes: |
text/plain |
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Label: |
MAX_20181212_KideneySections_AF488_1512_sim1024_029_SIR_PRJ.tif |
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Notes: |
image/tiff |
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Kidney_stack_CE1s-downscaled.tif |
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Notes: |
image/tiff |
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Label: |
Kidney_stack_CE1s.tif |
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Notes: |
image/tiff |
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Label: |
MAX_Kidney_CE1s-downscaled.tif |
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Notes: |
image/tiff |
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Label: |
MAX_Kidney_CE1s.tif |
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Notes: |
image/tiff |
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Label: |
Kidney_stack_MUSS-downscaled.tif |
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Notes: |
image/tiff |
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Label: |
Kidney_stack_MUSS.tif |
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Notes: |
image/tiff |
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Label: |
MAX_Kidney_MUSS-downscaled.tif |
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Notes: |
image/tiff |
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Label: |
MAX_Kidney_MUSS.tif |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_LTDR100nm-40m_1520_sim256_011_ch3_CE1s_t00-stack-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_LTDR100nm-40m_1520_sim256_011_ch3_CE1s_t00-stack.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_LTDR100nm-40m_1520_sim256_011_ch3_CE1s_t00-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_LTDR100nm-40m_1520_sim256_011_ch3_CE1s_t00.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_LTDR100nm-40m_1520_sim256_011_ch3_MUSS_t00-stack-downscaled.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
20210511_H9c2-dTag_GAL_LTDR100nm-40m_1520_sim256_011_ch3_MUSS_t00-stack.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_LTDR100nm-40m_1520_sim256_011_ch3_MUSS_t00-downscaled.tif |
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Text: | |
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image/tiff |
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Label: |
MAX_20210511_H9c2-dTag_GAL_LTDR100nm-40m_1520_sim256_011_ch3_MUSS_t00.tif |
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Text: | |
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Notes: |
image/tiff |
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Label: |
MAX_histogramEq-Norm_sim256_011_ch3_MUSS_t00.tif |
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Text: | |
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Notes: |
image/tiff |